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- EMDB-3706: Human cytoplasmic dynein-1 bound to dynactin and an N-terminal co... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-3706 | |||||||||
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Title | Human cytoplasmic dynein-1 bound to dynactin and an N-terminal construct of BICD2 | |||||||||
![]() | 3D reconstruction of DDB. Motor domains has The stable portion of the dynein tail is visible, whereas the motor domains are disordered. | |||||||||
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Function / homology | ![]() kinetochore => GO:0000776 / retrograde axonal transport of mitochondrion / dynactin complex / Regulation of PLK1 Activity at G2/M Transition / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / F-actin capping protein complex ...kinetochore => GO:0000776 / retrograde axonal transport of mitochondrion / dynactin complex / Regulation of PLK1 Activity at G2/M Transition / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / F-actin capping protein complex / negative regulation of filopodium assembly / dense body / dynein complex / Neutrophil degranulation / COPI-independent Golgi-to-ER retrograde traffic / coronary vasculature development / barbed-end actin filament capping / regulation of lamellipodium assembly / aorta development / Recruitment of NuMA to mitotic centrosomes / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / COPI-mediated anterograde transport / ventricular septum development / dynein complex binding / endoplasmic reticulum to Golgi vesicle-mediated transport / COPI-mediated anterograde transport / axon cytoplasm / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / mitotic spindle organization / cell morphogenesis / kinetochore / antigen processing and presentation of exogenous peptide antigen via MHC class II / actin filament binding / cell cortex / actin cytoskeleton organization / nuclear membrane / cytoskeleton / focal adhesion / centrosome / nucleoplasm / ATP binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.7 Å | |||||||||
![]() | Zhang K / Foster HE / Carter AP | |||||||||
![]() | ![]() Title: Cryo-EM Reveals How Human Cytoplasmic Dynein Is Auto-inhibited and Activated. Authors: Kai Zhang / Helen E Foster / Arnaud Rondelet / Samuel E Lacey / Nadia Bahi-Buisson / Alexander W Bird / Andrew P Carter / ![]() ![]() ![]() Abstract: Cytoplasmic dynein-1 binds dynactin and cargo adaptor proteins to form a transport machine capable of long-distance processive movement along microtubules. However, it is unclear why dynein-1 moves ...Cytoplasmic dynein-1 binds dynactin and cargo adaptor proteins to form a transport machine capable of long-distance processive movement along microtubules. However, it is unclear why dynein-1 moves poorly on its own or how it is activated by dynactin. Here, we present a cryoelectron microscopy structure of the complete 1.4-megadalton human dynein-1 complex in an inhibited state known as the phi-particle. We reveal the 3D structure of the cargo binding dynein tail and show how self-dimerization of the motor domains locks them in a conformation with low microtubule affinity. Disrupting motor dimerization with structure-based mutagenesis drives dynein-1 into an open form with higher affinity for both microtubules and dynactin. We find the open form is also inhibited for movement and that dynactin relieves this by reorienting the motor domains to interact correctly with microtubules. Our model explains how dynactin binding to the dynein-1 tail directly stimulates its motor activity. | |||||||||
History |
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Structure visualization
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 9.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 66.9 KB 66.9 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 12.7 KB | Display | ![]() |
Images | ![]() | 124.9 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 225.8 KB | Display | ![]() |
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Full document | ![]() | 224.9 KB | Display | |
Data in XML | ![]() | 12.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5nw4MC ![]() 3698C ![]() 3703C ![]() 3704C ![]() 3705C ![]() 3707C ![]() 5nugC ![]() 5nvsC ![]() 5nvuC C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | 3D reconstruction of DDB. Motor domains has The stable portion of the dynein tail is visible, whereas the motor domains are disordered. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.68 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
+Entire : Human cytoplasmic dynein-1 bound to dynactin and an N-terminal co...
+Supramolecule #1: Human cytoplasmic dynein-1 bound to dynactin and an N-terminal co...
+Supramolecule #2: dynein-1
+Supramolecule #3: dynactin
+Supramolecule #4: BICD2
+Macromolecule #1: dynein heavy chain
+Macromolecule #2: dynein intermediate chain
+Macromolecule #3: dynein intermediate chain
+Macromolecule #4: dynein heavy chain
+Macromolecule #5: dynein N-terminal dimerization domain
+Macromolecule #6: dynein N-terminal dimerization domain
+Macromolecule #7: Robl
+Macromolecule #8: dynein light intermediate chain
+Macromolecule #9: dynein light intermediate chain
+Macromolecule #10: Arp1
+Macromolecule #11: beta-actin
+Macromolecule #12: Arp11
+Macromolecule #13: Capping protein (Actin filament) muscle Z-line, alpha 1
+Macromolecule #14: F-actin capping protein beta subunit variant II
+Macromolecule #15: dynactin shoulder complex
+Macromolecule #16: dynactin shoulder complex
+Macromolecule #17: dynactin shoulder complex
+Macromolecule #18: dynactin shoulder complex
+Macromolecule #19: Dynactin 6
+Macromolecule #20: Dynactin subunit 5
+Macromolecule #21: dynactin pointed end p62
+Macromolecule #22: p150
+Macromolecule #23: Dynactin
+Macromolecule #24: Dynactin
+Macromolecule #25: Dynactin
+Macromolecule #26: Dynactin
+Macromolecule #27: dynactin p150
+Macromolecule #28: BICD2N
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 1.6 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |